0
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0
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624
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
15 months ago Fernanda • 0
0
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0
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474
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package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
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15 months ago Jane_Huang • 0
0
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2
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Question on performing ANOVA-like analysis using limma
limma
updated 15 months ago by 53k • written 15 months ago by • 0
0
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1
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504
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For feline genome
genomes Analysisoffelinegenome
updated 15 months ago by 68k • written 15 months ago by • 0
0
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1
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479
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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1
reply
653
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Rstudio died when put more than three letters in subseting a SummarizedExperiment object
SummarizedExperiment
15 months ago Shuo GG • 0
0
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0
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696
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Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
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15 months ago Cinque • 0
0
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2
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1.1k
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Harmonizing RNA-seq data of different sourceS(cell vs. tissue) to further conduct unsupervised clustering analysis?
HarmonizedTCGAData
written 15 months ago by • 0
1
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2
replies
718
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Inconsistent result in edgeR
edgeR
15 months ago hiroko.ohmiya • 0
0
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2
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802
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Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 16 months ago by • 0
1
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2
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843
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Student
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updated 15 months ago by ▴ 60 • written 15 months ago by • 0
2
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5
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1.2k
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Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
15 months ago ronin • 0
0
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13
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2.2k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 15 months ago by ▴ 20 • written 15 months ago by ▴ 10
17
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9
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How to use removeBatchEffect for removing effect of multiple confounding variables
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updated 15 months ago by 68k • written 9.6 years ago by ▴ 10
0
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523
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
15 months ago Alejandro • 0
0
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0
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933
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
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15 months ago Lluís Revilla Sancho ▴ 760
2
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2
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824
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How to read OSCA book?
BIOCON OSCA Bioconductor
15 months ago zr • 0
0
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1
reply
616
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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1
reply
660
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QSEA:Error in h(simpleError(msg, call))
qsea
15 months ago kf • 0
2
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1
reply
776
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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 15 months ago by 68k • written 15 months ago by ▴ 20
7
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9
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clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
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0
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Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
15 months ago Ragnhild • 0
0
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0
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726
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News: Metabolomics with R/Bioconductor Online Course
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15 months ago info ▴ 10
2
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1
reply
596
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object 'hdac_targets' not found
TPP
updated 15 months ago by 68k • written 15 months ago by • 0
1
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2
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869
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KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
15 months ago • updated 14 months ago Arindam ▴ 80
0
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Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 15 months ago by ▴ 70 • written 15 months ago by • 0
1
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2
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In the sesame package, what does the estimate output mean from testEnrichment()
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15 months ago ramiro.barrantes ▴ 10
0
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1
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643
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 15 months ago by ▴ 760 • written 15 months ago by • 0
1
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2
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812
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WARNING: No Bioconductor dependencies detected.
Bioconductor Biocon
15 months ago katja.danielzik • 0
0
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5
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Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
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0
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721
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 15 months ago by 68k • written 15 months ago by ▴ 10
0
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2
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PCA analysis RNA-Seq QC looks strange?
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updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
0
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concentration tables suitable as input for new packages?
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2
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0
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News: Save the Date for EuroBioC2025 in Barcelona!
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15 months ago Maria Doyle ▴ 110
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674
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Ideal approach to adjust for covariates for WGCNA
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updated 15 months ago by 68k • written 15 months ago by • 0
0
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5
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DESeq2 Multi-factor design not full rank
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written 4.6 years ago by • 0
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5
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ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
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updated 15 months ago by ▴ 760 • written 15 months ago by • 0
0
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0
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Job: Postdoctoral Research Associate in Computational Epigenomics
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15 months ago xiaolong • 0
0
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1
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by 6.7k • written 15 months ago by • 0
1
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1
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882
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 15 months ago by 53k • written 15 months ago by • 0
3
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6
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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2
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tximport data import
tximport
updated 15 months ago by 43k • written 15 months ago by • 0
2
votes
2
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877
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
0
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0
replies
709
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Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets differential-abundance
15 months ago 샤니쿠마리 • 0
2
votes
2
replies
1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
15 months ago Assa Yeroslaviz ★ 1.5k
1
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2
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 15 months ago by • 0
0
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4
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News: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
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updated 9 weeks ago by • 0 • written 15 months ago by ▴ 110
0
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1
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2.2k
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Unable to install/use limma
limma Bioconductor
updated 15 months ago by 68k • written 15 months ago by • 0
1
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3
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502 error biomaRt getLDS()
ensembldb biomaRt
updated 15 months ago by 68k • written 22 months ago by ▴ 10
1
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1
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825
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 15 months ago by 68k • written 15 months ago by • 0
1,000 results • Page 16 of 20
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Comment: Bioinformatician at the Lausanne University Hospital by TikTsokaasocissalpc • 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes by TikTsokaasocissalpc • 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers by Gordon Smyth 53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long? by ATpoint ★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Answer: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP by victor04052024 • 0
You write quite well, and the content is very interesting. I'll provide you a link to my page [granny 2](https://granny2.io).
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Limma-voom sample weights and impact on DEG numbers
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Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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